Jones spent the remainder of his time in Congress critical of efforts to send troops overseas, and fighting to end wars in Iraq and Afghanistan. He accused then-President George W. Bush for deceiving Congress to drum up support for overseas intervention.
As an attempt to atone for his vote in favor of the war, Jones sent letters to the families of nearly every soldier killed in Iraq and Afghanistan. Outside of his office, he posted pictures and bios of the more than 550 deceased troops that were sent to war from Camp Lejeune, located in his district.
In 2017, he told NPR that he had signed over 12,000 letters to the families of deceased troops, and "that was for me asking God to forgive me for my mistake." In a 2015 interview, he said he would "go to [his] grave" regretting his vote to start the Iraq War.
Jones is survived by his wife, Jo Annee, who he married in 1966, and his daughter, Ashley.